PURIFICATION OF RECOMBINANT PROTEINS by GEORGE CLIFFORD RUTT B.S., University of Arizona (1985) M.A., University of Alaska (1988) SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY December, 1996 ' " = e of Author '7.•- /-• ..... ------- T-------- !Departm'et of Chemical Engineering December 16, 1996 by YChesis Supervisor A. I by --------------------------------------- Chairman, Departmental Committee on Graduate Students APR 238 1997 ABSTRACT This project involved the design of a scaled-up process for the purification of a novel class of recombinant proteins, silk-elastin like proteins (SELP), which are block copolymers of the repeat amino acid sequence of silk (GAGAGS) and elastin (GVGVP). To facilitate process development, an HPLC assay for SELP was developed utilizing hydrophobic interaction chromatography which is less tedious and more quantitative then the existing assay. The purification protocol consists of flocculating cellular debris and anionic impurities, including nucleic acids, with a cationic polymer, followed by two sequential ammonium sulfate precipitations. This results in a 99.+ % purity of the SELP biopolymer. Two polymers, polyethyleneimine (PEI), and poly(dimethyldiallyl ammonium chloride) (PDMDAAC), were studied for impurity removal and flocculation properties. Optimal impurity removal correlated with optimal settling, and were found to be a function of pH and polymer concentration. The optimal condition for flocculation by PEI was found to be at a pH between 8 and 9, and a PEI concentration of 0.4 wt/vol % for lysate produced from 50 g/L dcw cells. PDMDAAC was determined to have significantly improved impurity removal and particulate settling characteristics at pH values above 11. A continuous polymer flocculation process is proposed, utilizing static mixers with continuous stirred tank particle aging, followed by centrifugation. The two sequential ammonium sulfate precipitation steps of SELP were characterized. Operating at 20% saturation (-0.8 M ammonium sulfate) is sufficient to precipitate three separate SELP species at yields greater then 99%. The ammonium sulfate precipitates have a spherical and highly deformable morphology. Precipitates from the second ammonium sulfate step are highly adhesive, suggesting the final design should incorporate features to avoid large losses during processing. In addition, HPLC-based techniques for characterizing product variability were developed. ACKNOWLEDGMENTS I would like to thank my thesis advisor, Professor Daniel Wang, for helping to advance both this thesis, and my own professional development during my tenure here at MIT. I am grateful for the many paths that his guidance has opened to me. Dr. Franco Ferrari and the people at Protein Polymer Technologies in San Diego provided raw materials, technical advice, and moral support for this project. I look forward with anticipation to interacting further with them. Communications with Rich Mathies at Alfa Laval Corporation helped me understand aspects of industrial centrifugation. Special thanks go to Jerry Sweeney, who assisted in the torturous task of final editing. Communications with the people of our research group proved invaluable for maintaining an enjoyable stay here. S. Meier, R. Balcarcel, J. Goswami, B. Follstad, G. Nyberg, A. Lamouse-Smith, M. Shelikoff, T. Simpson, J. Gargano, and S. Gu, will sorely be missed for the many shared technical and philosophical discourses. Special thanks go to Dr. John Chung, whose always available comments assisted in producing a better product. Additionally, Dr. Brian Kelley, and Eric Scharin provided helpful insight into industrial operations. Personal acknowledgments must go to people too numerous to mention here. I have been blessed with friends and family that support my efforts. Singling out a few individuals may only diminish the contributions of others. To all of you, I thank you deeply. TABLE OF CONTENTS LIST OF FIGURES 6 LIST OF TABLES 8 I. INTRODUCTION 9 II. OBJECTIVE 1 3 IIl. BACKGROUND 13 A. Silk Elastin Like Proteins (SELP) 13 B. Small-Scale Purification of SELP 15 C. Literature Survey on Precipitation 22 C.1 Precipitate Recovery 23 C.2 Formation of Precipitates by Polyelectrolytes 25 C.3 Formation of Precipitates by Salting-Out 29 IV. MATERIALS AND METHODS 43 A. Assay Development and SELP8K Characterization 44 B. Polyelectrolyte Precipitation 49 C. Ammonium Sulfate Precipitation 52 V. RESULTS AND DISCUSSION 56 A. Characterization of SELP8K 56 B. Polymer Flocculation B.1. Polyethyleneimine Precipitation 63 B.2. Poly(dimethyldiallyl ammonium chloride) 68 Precipitation B.3. Characterization of Solid-Liquid Separation 72 C. Ammonium Sulfate Precipitation of SELP Proteins 80 C.1. Effect of Temperature on SELP Solubility 80 C.2. Effect of Impurities on Solubility 84 C.3. Characterization of Solid Precipitate 87 VI. PROCESS SYNTHESIS 94 A. Cell Harvesting 97 B. Cell Disruption 99 C. Polymer Precipitation of Lysate 101 D. Ammonium Sulfate Precipitation 108 E Diafiltration/Ultrafiltration 112 F. Endotoxin Removal 113 G Product Formulation 114 VII. BIBLIOGRAPHY 115 LIST OF FIGURES Figure I: SELP8K Primary Amino Acid Sequence 14 Figure II: Small Scale SELP Purification Protocol 17 Figure Batch Scheduling of SELP Purification 18 IV: Figure IV: Process Volumes for Large Scale SELP 20 Purification Figure V: Precipitation Behavior of Two Hypothetical 33 Proteins Figure VI: Kinetic Competition Between Particle Nucleation 36 and Growth Figure VII: Hydrophobic Interaction Chromatography Behavior 45 of Different SELP Species Figure VIII. Immobilized Metal Affinity Chromatography 57 of SELP8K Figure IX. Cation Exchange Chromatography of SELP8K 59 and Results from Reinjection of Collected Peaks Figure X. Cation Exchange Chromatography of Cyanogen 60 Bromide Treated SELP8K Figure XI. Size Exclusion Behavior of SELP8K 62 Figure XII. Effect of Protein Concentration on the Size 63 Exclusion Behavior of SELP8K Figure XIII: Analysis of PEI Treated Lysate Supernatant, pH 7 64 Figure XIV: Effect of pH and PEI Concentration on the 67 Removal of Protein Impurities from Escherichia coli Derived Lysate Figure XV: Effect of pH and PDMDAAC Concentration on the 69 Removal of Protein Impurities from Escherichia coli Derived Lysate Figure XVI: Potential Mechanism of the pH Effect on PEI 75 Flocculation Figure XVII: Effect of Mixing and PEI Addition Rate on Settling 77 Behavior Figure XVIII: Comparison of the Extent of Settling of Lysate 78 Treated with PEI and PDMDAAC Polymers Figure XIX: Effect of Temperature on the Salting-out Curves 81 for Prepurified SELP8K, SELPOK, and SELPOK-CS1 Figure XX: Effect of Lysate Impurities on the Salting-out 84 Curves for SELP Figure XXI: Morphology of SELPOK Particles formed from the 89 Supernatant of Polymer Treated Lysate Figure XXII: Morphology of SELPOK Particles formed from 90 Prepurified Sources Figure XXIII: SELP Purification Process Flowsheet 95 Figure XXIV: SELP Purification Process Flow Diagram 96 Figure XXV: Proposed Configuration for Polyethyleneimine 104 Flocculation of Lysate Figure XXVI: Fed Batch Reactor for Ammonium Sulfate 109 Precipitation Figure XXVII: Schematic of a Typical Dia/ultrafiltration 113 Operation LIST OF TABLES Table I: Protein Purification Options 11 Table II: Cationic Polymer Characteristics 28 Table III: Concentration of Ammonium Sulfate at the 46 Apex of the SELP Elution Peak Table IV: SELP8K Yields at Various Conditions 70 Table V: Settling of PEI Treated Lysate, Measured by 73 Visual Observation at 15 minutes Table VI: Effect of Temperature on Parameters for the 82 Cohn Equation for Different SELP Species Table VII: Parameters for the Cohn Equation for Different 85 SELP Species Precipitated from the Supernatant of PEI Treated Lysate I. INTRODUCTION The recent development of recombinant DNA technology has enabled the production of a wide variety of polypeptide biopolymers in biochemical fermentation processes. The design of processes to purify these new biopolymers has relied for the most part on the scale-up of laboratory protocols. Batch processes are predominant, in part because of the batch nature of producing proteins by fermentation, and also due to the cost of reagents associated with potential continuous processes. Unlike processes involving small molecules, whose physical and chemical attributes can be predicted accurately, the ability to predict protein purification operations from first principles is untenable. This is due to the inherently complex nature of proteins, where subtle conformational changes can have tremendous impact on their physical characteristics. As a result, experiments at progressively larger scales of operation are essential to approach a final optimized process. Separation of a specific protein from cellular material consisting of carbohydrates, proteins, lipids, DNA, RNA, and assorted organic and inorganic moieties is inherently challenging. Often the protein of interest has characteristics similar to other components in the cell resulting in a difficult separation. The high purity required for biomedical applications often results in low yields, which translates to higher costs. Indeed, purification related cost can be up to 80-90% of the total production costs (Harrison, 1994). To minimize this cost, purification operations should be designed to take full advantage of any differential properties of the protein of interest. As shown in Table I, a number of purification operations exist to differentiate